MolNFT v1 · #157883 · protein
Crystal structure of the dark-adapted full-length bacteriophytochrome xccbphp mutant L193N from xanthomonas campestris
6NDO: “Crystal structure of the dark-adapted full-length bacteriophytochrome xccbphp mutant L193N from xanthomonas…”. X-ray diffraction, 1 ligand (BLA), 16 pockets (best druggability 0.84). MolNFT v1 #157883 on GenesisL1: 3D structure…
- PDB
- 6NDO
- Type
- protein
- Length
- 1,197 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bacteriophytochrome
- UniProt
- A0A0H2XCS3
- Ligands
- BLA
- Pockets
- 16 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bacteriophytochrome | protein | 593 | 34% helix, 25% strand | A0A0H2XCS3 |
| B | Bacteriophytochrome | protein | 604 | 34% helix, 24% strand | A0A0H2XCS3 |
Ligands and binding sites
- BLA · Biliverdine IX alpha · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 958 | 0.84 | 0.86 | 81 | empty |
| 2 | 285 | 0.81 | 0.92 | 40 | BLA |
| 3 | 251 | 0.80 | 0.92 | 31 | BLA |
| 4 | 358 | 0.77 | 0.87 | 31 | empty |
| 5 | 391 | 0.62 | 0.77 | 49 | empty |
Interfaces
1 interface between chains.
- A–B · 3305 Ų buried · 42 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (biliverdin attachment).
Compared structures
- 6NDO · Crystal structure of the dark-adapted full-length bacteriophytochrome XccBphP mutant… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt A0A0H2XCS3
- Elsewhere: RCSB PDB 6NDO · PDBe 6NDO · UniProt A0A0H2XCS3
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